PathogenSeq: TBDR

This tool processes raw sequence data to infer strain type and identify known drug resistance markers.

A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.

This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.

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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).

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Summary

ID: 5cc54d3a4e2da

Date: Sun Apr 28 07:51:38 2019

Strain: lineage2;lineage4.3.1;lineage3.1.2.2

Drug-resistance: Sensitive

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid

Rifampicin

Ethambutol

Pyrazinamide

Streptomycin

Ethionamide

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

lineage2 East-Asian Beijing RD105

lineage4.3.1 Euro-American (LAM) LAM9 None

lineage3.1.2.2 East-African-Indian CAS RD750

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrA	7362	p.Glu21Gln	1.000
gyrA	7391	c.90C>T	1.000
gyrA	7394	c.93T>C	1.000
gyrA	7397	c.96G>C	1.000
gyrA	7406	c.105G>C	1.000
gyrA	7412	c.111C>G	1.000
gyrA	7418	c.117C>T	1.000
gyrA	7433	c.132G>A	1.000
gyrA	7442	c.141G>C	1.000
gyrA	7457	c.156T>C	1.000
gyrA	7463	c.162G>C	1.000
gyrA	7472	c.171T>C	1.000
gyrA	7475	c.174A>G	1.000
gyrA	7480	p.Phe60Tyr	1.000
gyrA	7484	c.183T>C	1.000
gyrA	7499	c.198G>C	1.000
gyrA	7526	c.225G>C	1.000
gyrA	7532	c.231T>G	1.000
gyrA	7541	c.240C>G	1.000
gyrA	7547	c.246C>T	1.000
gyrA	7565	c.264C>T	1.000
gyrA	7569	p.Ala90Ser	1.000
gyrA	7585	p.Ser95Thr	1.000
gyrA	8294	c.993T>C	1.000
gyrA	8324	c.1023T>C	1.000
gyrA	8327	c.1026C>G	1.000
gyrA	8339	c.1038A>G	1.000
gyrA	8340	p.Ala347Ser	1.000
gyrA	8354	c.1053G>C	1.000
gyrA	8366	c.1065G>C	1.000
gyrA	8372	c.1071G>T	1.000
rpoB	760181	c.375T>C	1.000
rpoB	760184	c.378A>G	1.000
rpoB	760196	c.390C>G	1.000
rpoB	760235	c.429T>C	1.000
rpoB	760244	c.438G>C	1.000
rpoB	760283	c.477G>C	1.000
rpoB	760298	c.492G>C	1.000
rpoB	760430	c.624T>C	1.000
rpoB	760433	c.627C>T	1.000
rpoB	760457	c.651C>T	1.000
rpoB	760463	c.657C>T	1.000
rpoB	761213	c.1407G>C	1.000
rpoB	761249	c.1443A>G	1.000
rpoB	761261	c.1455G>T	1.000
rpoB	761264	c.1458C>G	1.000
rpoB	761282	c.1476C>T	1.000
rpoB	761288	c.1482G>T	1.000
rpoB	761318	c.1512G>T	1.000
rpoB	761327	c.1521A>G	1.000
rpoB	761330	c.1524G>C	1.000
rpoB	761552	c.1746G>C	1.000
rpoB	761555	c.1749G>C	1.000
rpoB	761558	c.1752C>G	1.000
rpoB	761570	c.1764T>C	1.000
rpoB	761573	c.1767C>G	1.000
rpoB	761579	c.1773G>C	1.000
rpoB	761606	c.1800C>G	1.000
rpoB	761612	c.1806G>T	1.000
rpoB	761615	c.1809A>C	1.000
rpoB	761636	c.1830G>T	1.000
rpoB	761969	c.2163G>A	1.000
rpoB	762008	c.2202C>T	1.000
rpoB	762014	c.2208C>T	1.000
rpoB	762047	c.2241G>A	1.000
rpoB	762053	c.2247T>C	1.000
rpoB	762065	c.2259T>C	1.000
rpoB	762083	c.2277T>C	1.000
rpoB	762086	c.2280G>C	1.000
rpoB	762101	c.2295C>G	1.000
rpoB	762114	p.Ile770Val	1.000
rpoB	762158	c.2352G>C	1.000
rpoB	762185	c.2379G>C	1.000
rpoB	762224	c.2418C>G	1.000
rpoB	762233	c.2427G>C	1.000
rpoB	762245	c.2439G>C	1.000
rpoB	762833	c.3027C>T	1.000
rpoB	762839	c.3033G>A	1.000
rpoB	762857	c.3051C>G	1.000
rpoB	762863	c.3057T>C	1.000
rpoB	762879	p.Met1025Leu	1.000
rpoB	762917	c.3111C>G	1.000
rpoB	762920	c.3114C>T	1.000
rpoB	762929	c.3123G>C	1.000
rpoB	762959	c.3153G>C	1.000
rpoB	762962	c.3156C>T	1.000
rpoB	762995	c.3189G>T	0.917
rpoB	763004	c.3198G>A	1.000
rpoB	763007	c.3201C>T	1.000
rpoB	763022	c.3216C>G	1.000
rpoB	763028	c.3222T>C	1.000
rpoB	763031	c.3225T>G	1.000
rpoB	763053	c.3247T>C	1.000
rpoB	763070	c.3264T>C	1.000
rpoB	763085	c.3279C>G	1.000
rpoB	763103	c.3297G>C	1.000
rpoB	763115	c.3309T>C	1.000
rpoB	763127	c.3321G>C	1.000
rpoB	763130	c.3324G>A	1.000
rpoB	763133	c.3327G>C	1.000
rpoB	763136	c.3330C>T	1.000
rpoB	763142	c.3336C>G	1.000
rpoB	763160	c.3354G>T	1.000
rpoC	763456	c.87A>G	1.000
rpoC	763468	c.99G>C	1.000
rpoC	763486	c.117T>C	1.000
rpoC	763492	c.123G>T	1.000
rpoC	763528	c.159G>A	1.000
rpoC	763546	c.177A>G	1.000
rpoC	763558	c.189C>T	1.000
rpoC	763570	c.201G>C	1.000
rpoC	763573	c.204G>C	1.000
rpoC	763594	c.225C>T	1.000
rpoC	763603	c.234C>T	1.000
rpoC	763615	c.246G>C	1.000
rpoC	763618	c.249C>T	1.000
rpoC	763633	c.264T>C	1.000
rpoC	763660	c.291T>G	1.000
rpoC	763666	c.297G>A	1.000
rpoC	763675	c.306C>G	1.000
rpoC	763765	c.396T>G	1.000
rpoC	763792	p.Glu141Asp	1.000
rpoC	763807	c.438T>C	1.000
rpoC	763813	c.444C>G	1.000
rpoC	764500	c.1131C>G	1.000
rpoC	764521	c.1152T>C	1.000
rpoC	764536	c.1167G>T	1.000
rpoC	764539	c.1170C>G	1.000
rpoC	764575	c.1206T>G	1.000
rpoC	764605	c.1236G>C	1.000
rpoC	764611	c.1242G>T	1.000
rpoC	764623	c.1254C>G	1.000
rpoC	764626	c.1257C>T	1.000
rpoC	764632	c.1263T>C	1.000
rpoC	764650	c.1281G>T	1.000
rpoC	764701	c.1332C>G	1.000
rpoC	764713	c.1344G>T	1.000
rpoC	764716	c.1347G>C	1.000
rpoC	764746	c.1377G>T	1.000
rpoC	764752	c.1383G>C	1.000
rpoC	764758	c.1389C>G	1.000
rpoC	764764	c.1395T>C	1.000
rpoC	764803	c.1434C>T	1.000
rpoC	764809	c.1440C>T	1.000
rpoC	764815	c.1446A>G	1.000
rpoC	764824	c.1455T>C	1.000
rpoC	764827	c.1458G>C	1.000
rpoC	764851	c.1482C>T	1.000
rpoC	764858	c.1489T>C	1.000
rpoC	764869	c.1500C>T	1.000
rpoC	764875	c.1506C>T	1.000
rpoC	764878	c.1509C>G	1.000
rpoC	764887	c.1518G>C	1.000
rpoC	764888	c.1519T>C	1.000
rpoC	764911	c.1542A>G	1.000
rpoC	764912	p.Met515Gln	1.000
rpoC	764932	c.1563C>A	0.938
rpoC	764935	c.1566T>C	1.000
rpoC	764948	c.1579T>C	1.000
rpoC	764968	c.1599T>C	1.000
rpoC	765466	c.2097C>T	1.000
rpoC	765478	c.2109T>C	1.000
rpoC	765480	p.Tyr704Phe	1.000
rpoC	765496	c.2127C>G	1.000
rpoC	765811	c.2442T>G	1.000
rpoC	765814	c.2445A>C	1.000
rpoC	765817	c.2448G>C	1.000
rpoC	765823	c.2454C>A	1.000
rpoC	765826	c.2457T>C	1.000
rpoC	765835	c.2466C>T	1.000
rpoC	765871	c.2502T>C	1.000
rpoC	765875	p.Val836Ile	1.000
rpoC	765886	c.2517C>G	1.000
rpoC	765904	c.2535C>G	1.000
rpoC	765908	c.2539C>T	1.000
rpsL	781628	c.69T>C	1.000
rpsL	781631	c.72G>C	1.000
rpsL	781649	c.90T>C	1.000
rpsL	781655	c.96T>C	1.000
rpsL	781658	c.99A>G	1.000
rpsL	781682	c.123T>C	1.000
rpsL	781709	c.150G>C	1.000
rpsL	781715	c.156T>C	1.000
rpsL	781760	c.201T>C	1.000
rpsL	781772	c.213C>T	1.000
rpsL	781808	c.249C>T	1.000
rpsL	781814	c.255C>T	1.000
rpsL	781817	c.258G>T	1.000
rpsL	781829	c.270G>C	1.000
rpsL	781832	c.273T>C	1.000
rpsL	781838	c.279G>C	1.000
rpsL	781841	c.282C>T	1.000
rpsL	781859	c.300T>G	1.000
rpsL	781865	c.306G>C	1.000
rpsL	781868	c.309T>C	1.000
rpsL	781871	c.312G>C	1.000
rpsL	781892	c.333A>G	1.000
rpsL	781898	c.339A>C	1.000
rpsL	781901	c.342C>T	1.000
rpsL	781907	c.348T>C	1.000
rpsL	781916	c.357T>C	1.000
rpsL	781929	p.Gly124Ser	1.000
rrs	1471922	r.77gt>g	1.000
rrs	1471925	r.80t>c	1.000
rrs	1471931	r.86ga>g	1.000
rrs	1471933	r.88ga>g	1.000
rrs	1471934	r.89a>g	1.000
rrs	1471986	r.141c>t	1.000
rrs	1472019	r.174g>a	1.000
rrs	1472023	r.178g>t	1.000
rrs	1472031	r.186g>c	1.000
rrs	1472053	r.208agc>a	1.000
rrs	1472061	r.216a>t	1.000
rrs	1472075	r.230a>g	1.000
rrs	1472106	r.261g>a	1.000
rrs	1472108	r.263c>t	1.000
rrs	1472150	r.305t>a	1.000
rrs	1472251	r.406g>a	1.000
rrs	1472337	r.492c>g	1.000
rrs	1472380	r.535g>c	1.000
rrs	1472446	r.601t>a	0.950
rrs	1472452	r.607g>a	0.974
rrs	1472464	r.619a>g	1.000
rrs	1472846	r.1001c>a	1.000
rrs	1472847	r.1002g>c	0.941
rrs	1472849	r.1004c>g	1.000
rrs	1472850	r.1005t>c	1.000
rrs	1472857	r.1012a>g	1.000
rrs	1472858	r.1013g>t	1.000
rrs	1472860	r.1015c>g	1.000
rrs	1472861	r.1016g>t	1.000
rrs	1472973	r.1128a>t	1.000
rrs	1473104	r.1259c>t	0.972
rrs	1473110	r.1265t>g	1.000
rrs	1473111	r.1266a>g	1.000
rrs	1473120	r.1275c>ct	0.865
rrs	1473123	r.1278a>c	1.000
rrs	1473276	r.1431a>g	1.000
rrs	1473290	r.1445c>t	1.000
rrs	1473291	r.1446g>gt	1.000
rrs	1473301	r.1456t>c	1.000
rrl	1473668	r.11c>t	1.000
rrl	1473696	r.39t>c	1.000
rrl	1473697	r.40c>t	1.000
rrl	1473699	r.42a>g	1.000
rrl	1473717	r.60g>t	0.963
rrl	1473746	r.89t>c	1.000
rrl	1473758	r.101g>t	1.000
rrl	1473770	r.113t>g	1.000
rrl	1473788	r.131a>g	1.000
rrl	1473876	r.219g>a	1.000
rrl	1473887	r.230t>a	1.000
rrl	1473898	r.241c>t	1.000
rrl	1473899	r.242a>g	1.000
rrl	1473916	r.259c>a	1.000
rrl	1474135	r.478g>a	0.957
rrl	1474140	r.483c>t	0.957
rrl	1474151	r.494c>t	0.960
rrl	1474174	r.517a>g	0.962
rrl	1474181	r.524c>t	1.000
rrl	1474183	r.526t>c	1.000
rrl	1474185	r.528g>a	1.000
rrl	1474186	r.529a>g	1.000
rrl	1474249	r.592g>t	1.000
rrl	1474266	r.609t>c	1.000
rrl	1474269	r.612c>t	1.000
rrl	1474310	r.653t>g	1.000
rrl	1474362	r.705a>g	1.000
rrl	1474446	r.789c>t	1.000
rrl	1474673	r.1016t>c	1.000
rrl	1474676	r.1019t>a	1.000
rrl	1474677	r.1020a>g	1.000
rrl	1474720	r.1063c>t	1.000
rrl	1474753	r.1096a>g	1.000
rrl	1474760	r.1103a>g	1.000
rrl	1474794	r.1137c>t	1.000
rrl	1474803	r.1146g>a	1.000
rrl	1474812	r.1155g>a	1.000
rrl	1474830	r.1173a>g	1.000
rrl	1474932	r.1275c>t	1.000
rrl	1475031	r.1374g>t	1.000
rrl	1475061	r.1404c>a	1.000
rrl	1475062	r.1405a>t	1.000
rrl	1475120	r.1463g>t	1.000
rrl	1475315	r.1658a>t	1.000
rrl	1475353	r.1696a>t	1.000
rrl	1475354	r.1697a>g	1.000
rrl	1475355	r.1698c>t	1.000
rrl	1475363	r.1706c>t	1.000
rrl	1475369	r.1712g>t	1.000
rrl	1475419	r.1762c>t	1.000
rrl	1475429	r.1772g>t	1.000
rrl	1475452	r.1795c>a	1.000
rrl	1475479	r.1822c>g	1.000
rrl	1475483	r.1826c>t	1.000
rrl	1475505	r.1848g>a	1.000
rrl	1475526	r.1869c>a	1.000
rrl	1475531	r.1874c>t	1.000
rrl	1475544	r.1887a>t	1.000
rrl	1475545	r.1888t>g	1.000
rrl	1475659	r.2002g>a	1.000
rrl	1475753	r.2096c>t	1.000
rrl	1475762	r.2105g>t	1.000
rrl	1475763	r.2106c>t	1.000
rrl	1475764	r.2107a>c	1.000
rrl	1475765	r.2108a>g	1.000
rrl	1475775	r.2118g>a	1.000
rrl	1475988	r.2331a>g	1.000
rrl	1475991	r.2334t>c	1.000
rrl	1475995	r.2338g>a	1.000
rrl	1476088	r.2431a>c	0.947
rrl	1476099	r.2442a>g	0.933
rrl	1476103	r.2446c>g	0.933
rrl	1476105	r.2448g>a	0.933
rrl	1476106	r.2449a>t	0.933
rrl	1476110	r.2453g>c	0.933
rrl	1476115	r.2458t>c	0.941
rrl	1476131	r.2474c>t	0.964
rrl	1476160	r.2503t>c	1.000
rrl	1476214	r.2557g>t	1.000
rrl	1476215	r.2558c>t	1.000
rrl	1476224	r.2567a>g	1.000
rrl	1476251	r.2594t>g	0.971
rrl	1476256	r.2599a>t	1.000
rrl	1476260	r.2603a>g	1.000
rrl	1476281	r.2624t>c	1.000
rrl	1476297	r.2640c>t	1.000
rrl	1476299	r.2642c>t	1.000
rrl	1476529	r.2872a>g	1.000
rrl	1476540	r.2883c>t	1.000
rrl	1476583	r.2926g>a	1.000
rrl	1476584	r.2927c>t	1.000
rrl	1476594	r.2937c>t	1.000
rrl	1476597	r.2940g>a	1.000
rrl	1476603	r.2946g>a	1.000
rrl	1476628	r.2971t>a	1.000
rrl	1476664	r.3007t>c	1.000
rrl	1476665	r.3008t>c	1.000
rrl	1476674	r.3017t>c	1.000
rrl	1476679	r.3022t>c	1.000
rrl	1476689	r.3032a>t	1.000
rrl	1476690	r.3033c>t	1.000
rrl	1476693	r.3036g>a	1.000
rrl	1476695	r.3038t>a	1.000
rpsA	1833616	c.75A>C	1.000
rpsA	1833619	c.78A>C	1.000
rpsA	1833628	c.87G>C	1.000
rpsA	1833634	c.93G>A	1.000
rpsA	1833894	p.Ala118Glu	1.000
rpsA	1833904	c.363G>A	1.000
rpsA	1833928	c.387G>C	1.000
rpsA	1833949	c.408T>C	1.000
rpsA	1833970	c.429G>T	1.000
rpsA	1833976	c.435C>T	1.000
rpsA	1833979	c.438T>C	1.000
rpsA	1833991	c.450C>A	1.000
rpsA	1834000	c.459G>C	1.000
rpsA	1834009	c.468C>T	1.000
rpsA	1834012	c.471G>T	1.000
rpsA	1834015	c.474G>C	1.000
rpsA	1834021	c.480C>T	1.000
rpsA	1834030	c.489C>G	1.000
rpsA	1834078	c.537C>T	1.000
rpsA	1834097	c.556T>A	1.000
rpsA	1834102	c.561T>C	1.000
rpsA	1834177	c.636A>C	1.000
rpsA	1834189	c.648G>C	1.000
rpsA	1834213	c.672G>C	1.000
rpsA	1834234	c.693G>C	1.000
rpsA	1834240	c.699T>C	1.000
rpsA	1834246	c.705G>C	1.000
rpsA	1834249	c.708T>C	1.000
rpsA	1834252	c.711C>G	1.000
rpsA	1834261	c.720A>G	1.000
rpsA	1834264	c.723G>C	1.000
rpsA	1834279	c.738C>T	1.000
rpsA	1834297	c.756C>T	1.000
rpsA	1834303	c.762T>G	1.000
rpsA	1834366	c.825A>G	1.000
rpsA	1834411	c.870T>C	1.000
rpsA	1834423	c.882G>T	1.000
rpsA	1834451	c.910T>C	1.000
rpsA	1834456	c.915T>G	1.000
rpsA	1834606	c.1065C>T	1.000
rpsA	1834609	c.1068T>C	1.000
rpsA	1834619	c.1078T>C	1.000
rpsA	1834622	c.1081T>A	1.000
rpsA	1834633	c.1092A>G	1.000
rpsA	1834639	c.1098T>C	1.000
rpsA	1834666	c.1125G>C	1.000
rpsA	1834667	p.Ala376Ser	1.000
rpsA	1834690	c.1149T>C	1.000
rpsA	1834732	c.1191T>C	1.000
rpsA	1834738	c.1197A>G	1.000
rpsA	1834753	c.1212T>C	1.000
rpsA	1834756	c.1215G>A	1.000
rpsA	1834759	c.1218A>C	1.000
rpsA	1834765	p.Glu408Asp	1.000
rpsA	1834774	c.1233C>G	1.000
rpsA	1834776	p.Ala412Glu	1.000
rpsA	1834780	c.1239A>G	1.000
rpsA	1834786	c.1245A>G	1.000
rpsA	1834789	c.1248T>C	1.000
rpsA	1834792	c.1251G>C	1.000
embC	4240717	c.855T>C	1.000
embC	4240768	c.906G>A	1.000
embC	4240780	c.918T>C	1.000
embC	4240783	c.921G>C	1.000
embC	4240786	c.924C>T	1.000
embC	4240789	c.927T>C	1.000
embC	4240819	c.957A>C	1.000
embC	4240828	c.966G>A	1.000
embC	4240831	c.969T>G	1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

Analysis	Program
Mapping	bwa
Variant Calling	BCFtools

Log

Drug Details

The estimated accuracy of drug resistance predictions is:

Drug¹	Sensitivity (%)	Specificity (%)
Isoniazid	92.8 (89.9-95.7)	100 (100-100)
Rifampicin	96.2 (93.9-98.5)	98.1 (96.8-99.4)
Ethambutal	88.7 (83.6-93.8)	81.7 (77.6-85.8)
Pyrazinamide	70.9 (62.4-79.4)	93.9 (90.6-97.2)
Streptomycin	87.1 (82.7-91.5)	89.7 (86.0-93.4)
Ethionamide	73.6 (66.7-80.5)	93.3 (89.6-97.0)
Moxifloxacin	60.0 (29.6-90.4)	68.7 (52.6-84.8)
Ofloxacin	85.5 (79.1-91.9)	94.9 (91.8-98.0)
Amikacin	82.9 (74.4-91.4)	98.3 (96.0-100)
Capreomycin	60.7 (50.6-70.8)	90.7 (87.2-94.2)
Kanamycin	87.3 (81.3-93.3)	93.4 (89.9-96.9)
Para-aminosalisylic acid	Not determined	Not determined
Linezolid	Not determined	Not determined
Clofazimine	Not determined	Not determined
Bedaquiline	Not determined	Not determined
Multi drug resistance	91.2 (87.8-94.6)	98.4 (97.2-99.6)
Extremely drug resistance	75.9 (64.5-87.3)	98.4 (97.3-99.5)

Lineages

Lineage²	Location	Strain	RD type
lineage1	Indo-Oceanic	EAI	RD239
lineage1.1	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
lineage1.1.1	Indo-Oceanic	EAI4;EAI5	RD239
lineage1.1.1.1	Indo-Oceanic	EAI4;ZERO	RD239
lineage1.1.2	Indo-Oceanic	EAI3;EAI5	RD239
lineage1.1.3	Indo-Oceanic	EAI6	RD239
lineage1.2	Indo-Oceanic	EAI1;EAI2	RD239
lineage1.2.1	Indo-Oceanic	EAI2	RD239
lineage1.2.2	Indo-Oceanic	EAI1	RD239
lineage2	East-Asian	Beijing	RD105
lineage2.1	East-Asian (non-Beijing)	None	None
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
lineage2.2.1.2	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
lineage2.2.1.1	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
lineage3	East-African-Indian	CAS	RD750
lineage3.1	East-African-Indian	Non-CAS1-Delhi	RD750
lineage3.1.1	East-African-Indian	CAS1-Kili	RD750
lineage3.1.2	East-African-Indian	CAS;CAS2	RD750
lineage3.1.2.1	East-African-Indian	CAS2	RD750
lineage3.1.2.2	East-African-Indian	CAS	RD750
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.1	Euro-American	T;X;H	None
lineage4.1.2	Euro-American (X-type)	T;H	None
lineage4.1.2.1	Euro-American (X-type)	T1;H1	RD182
lineage4.1.1	Euro-American (X-type)	X1;X2;X3	None
lineage4.1.1.2	Euro-American (X-type)	X1	None
lineage4.1.1.1	Euro-American (X-type)	X2	RD183
lineage4.1.1.3	Euro-American (Haarlem)	X1;X3	RD193
lineage4.2	Euro-American	H;T;LAM	None
lineage4.2.2	Euro-American (Ural)	T;LAM7-TUR	None
lineage4.2.2.1	Euro-American	LAM7-TUR	None
lineage4.2.1	Euro-American (TUR)	H3;H4	None
lineage4.3	Euro-American (LAM)	mainly-LAM	None
lineage4.3.1	Euro-American (LAM)	LAM9	None
lineage4.3.3	Euro-American (LAM)	LAM;T	RD115
lineage4.3.4	Euro-American (LAM)	LAM	RD174
lineage4.3.4.1	Euro-American (LAM)	LAM1;LAM2	RD174
lineage4.3.4.2	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
lineage4.3.4.2.1	Euro-American (LAM)	LAM11	RD174
lineage4.3.2	Euro-American (LAM)	LAM3	None
lineage4.3.2.1	Euro-American (LAM)	LAM3	RD761
lineage4.4	Euro-American	S;T	None
lineage4.4.2	Euro-American	T1;T2	None
lineage4.4.1	Euro-American (S-type)	S;T	None
lineage4.4.1.2	Euro-American	T1	None
lineage4.4.1.1	Euro-American	S;Orphans	None
lineage4.5	Euro-American	H;T	RD122
lineage4.6	Euro-American	T;LAM	None
lineage4.6.1	Euro-American (Uganda)	T2	RD724
lineage4.6.1.1	Euro-American	T2-Uganda	RD724
lineage4.6.1.2	Euro-American	T2	RD724
lineage4.6.2	Euro-American	T;LAM	RD726
lineage4.6.2.1	Euro-American	T3	RD726
lineage4.6.2.2	Euro-American (Cameroon)	LAM10-CAM	RD726
lineage4.7	Euro-American (mainly T)	T1;T5	None
lineage4.8	Euro-American (mainly T)	T1;T2;T3;T5	RD219
lineage4.9	Euro-American (H37Rv-like)	T1	None
lineage5	West-Africa 1	AFRI_2;AFRI_3	RD711
lineage6	West-Africa 2	AFRI_1	RD702
lineage7	Lineage 7	None	None
lineageBOV	M. bovis	BOV_1;BOV_2	None

Citations

1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer

This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.

Drug¹	Resistance	Supporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage²	Family	Main Spoligotype	RDS
lineage2	East-Asian	Beijing	RD105
lineage4.3.1	Euro-American (LAM)	LAM9	None
lineage3.1.2.2	East-African-Indian	CAS	RD750